Sex expression and floral morphology studies are central to understand breeding behavior and to define the productive potential of plant genotypes. In particular, the new bioenergy crop Jatropha curcas L. has been classified as a monoecious species. Nonetheless, there is no information about its reproductive diversity in the Mesoamerican region, which is considered its center of origin and diversification. Thus, we determined sex expression and floral morphology in J. curcas populations from southern Mexico and Guatemala. Our results showed that most of J. curcas specimens had typical inflorescences separate sexes (monoecious), meanwhile the rest were atypical (gynoecious, androecious, andromonoecious, androgynomonoecious). The most important variables to group these populations, based on a discriminant analysis, were: male flower diameter, female petal length and male nectary length. From the southern Mexico "Guerrero" was the most diverse population and in Chiapas "Centro". On the other hand, a cluster analysis showed that the accessions from southern Mexico were grouped without showing any correlation with the geographical origin, while those accessions with atypical sexuality were grouped together. Additionally, a Mantel test showed a significant correlation between the distance matrix generated in this study and the genetic distance matrix (AFLP) previously reported for the same accessions. Our results contribute to design genetic improvement programs by using sexually and morphologically contrasting plants from the center of origin.